Literature DB >> 21501817

Atomic resolution cryo electron microscopy of macromolecular complexes.

Z Hong Zhou1.   

Abstract

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their "native," noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines.
Copyright © 2011 Elsevier Inc. All rights reserved.

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Year:  2011        PMID: 21501817      PMCID: PMC3698602          DOI: 10.1016/B978-0-12-386507-6.00001-4

Source DB:  PubMed          Journal:  Adv Protein Chem Struct Biol        ISSN: 1876-1623            Impact factor:   3.507


  105 in total

1.  EMAN: semiautomated software for high-resolution single-particle reconstructions.

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2.  Structural rearrangements in the membrane penetration protein of a non-enveloped virus.

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Journal:  Nature       Date:  2004-08-26       Impact factor: 49.962

3.  The dsRNA viruses.

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4.  FREALIGN: high-resolution refinement of single particle structures.

Authors:  Nikolaus Grigorieff
Journal:  J Struct Biol       Date:  2006-06-02       Impact factor: 2.867

5.  CTF determination of images of ice-embedded single particles using a graphics interface.

Authors:  Z H Zhou; S Hardt; B Wang; M B Sherman; J Jakana; W Chiu
Journal:  J Struct Biol       Date:  1996 Jan-Feb       Impact factor: 2.867

6.  Three-dimensional structure of vinculin bound to actin filaments.

Authors:  Mandy E W Janssen; Eldar Kim; Hongjun Liu; L Miya Fujimoto; Andrey Bobkov; Niels Volkmann; Dorit Hanein
Journal:  Mol Cell       Date:  2006-01-20       Impact factor: 17.970

7.  Structural analysis of a fiber-pseudotyped adenovirus with ocular tropism suggests differential modes of cell receptor interactions.

Authors:  C Y Chiu; E Wu; S L Brown; D J Von Seggern; G R Nemerow; P L Stewart
Journal:  J Virol       Date:  2001-06       Impact factor: 5.103

8.  Assembly of VP26 in herpes simplex virus-1 inferred from structures of wild-type and recombinant capsids.

Authors:  Z H Zhou; J He; J Jakana; J D Tatman; F J Rixon; W Chiu
Journal:  Nat Struct Biol       Date:  1995-11

9.  Cryo-EM reconstruction of dengue virus in complex with the carbohydrate recognition domain of DC-SIGN.

Authors:  Elena Pokidysheva; Ying Zhang; Anthony J Battisti; Carol M Bator-Kelly; Paul R Chipman; Chuan Xiao; G Glenn Gregorio; Wayne A Hendrickson; Richard J Kuhn; Michael G Rossmann
Journal:  Cell       Date:  2006-02-10       Impact factor: 41.582

10.  Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics.

Authors:  Lingpeng Cheng; Jiang Zhu; Wong Hoi Hui; Xiaokang Zhang; Barry Honig; Qin Fang; Z Hong Zhou
Journal:  J Mol Biol       Date:  2009-12-28       Impact factor: 5.469

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  30 in total

1.  Visualizing proteins and macromolecular complexes by negative stain EM: from grid preparation to image acquisition.

Authors:  David S Booth; Agustin Avila-Sakar; Yifan Cheng
Journal:  J Vis Exp       Date:  2011-12-22       Impact factor: 1.355

Review 2.  X-ray crystallography over the past decade for novel drug discovery - where are we heading next?

Authors:  Heping Zheng; Katarzyna B Handing; Matthew D Zimmerman; Ivan G Shabalin; Steven C Almo; Wladek Minor
Journal:  Expert Opin Drug Discov       Date:  2015-07-15       Impact factor: 6.098

3.  Atomic structure of the human cytomegalovirus capsid with its securing tegument layer of pp150.

Authors:  Xuekui Yu; Jonathan Jih; Jiansen Jiang; Z Hong Zhou
Journal:  Science       Date:  2017-06-30       Impact factor: 47.728

4.  Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images.

Authors:  Javier Velázquez-Muriel; Keren Lasker; Daniel Russel; Jeremy Phillips; Benjamin M Webb; Dina Schneidman-Duhovny; Andrej Sali
Journal:  Proc Natl Acad Sci U S A       Date:  2012-10-29       Impact factor: 11.205

5.  3D imaging and quantitative analysis of small solubilized membrane proteins and their complexes by transmission electron microscopy.

Authors:  Ardeschir Vahedi-Faridi; Beata Jastrzebska; Krzysztof Palczewski; Andreas Engel
Journal:  Microscopy (Oxf)       Date:  2012-12-23       Impact factor: 1.571

6.  Unified polymerization mechanism for the assembly of ASC-dependent inflammasomes.

Authors:  Alvin Lu; Venkat Giri Magupalli; Jianbin Ruan; Qian Yin; Maninjay K Atianand; Matthijn R Vos; Gunnar F Schröder; Katherine A Fitzgerald; Hao Wu; Edward H Egelman
Journal:  Cell       Date:  2014-03-13       Impact factor: 41.582

7.  Single particle analysis integrated with microscopy: a high-throughput approach for reconstructing icosahedral particles.

Authors:  Xiaodong Yan; Giovanni Cardone; Xing Zhang; Z Hong Zhou; Timothy S Baker
Journal:  J Struct Biol       Date:  2014-03-05       Impact factor: 2.867

8.  Creating an infrastructure for high-throughput high-resolution cryogenic electron microscopy.

Authors:  Donald C Shrum; Brent W Woodruff; Scott M Stagg
Journal:  J Struct Biol       Date:  2012-07-25       Impact factor: 2.867

Review 9.  Structural biology of TRP channels.

Authors:  Ute A Hellmich; Rachelle Gaudet
Journal:  Handb Exp Pharmacol       Date:  2014

10.  Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale.

Authors:  Guray Kuzu; Attila Gursoy; Ruth Nussinov; Ozlem Keskin
Journal:  J Proteome Res       Date:  2013-04-30       Impact factor: 4.466

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